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[cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]


Chronological Thread 
  • From: lpsmith at spod-central.org (Lucian Smith)
  • Subject: [cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]
  • Date: Thu, 3 Jun 2010 20:45:26 +0100
My only comment is that lines 6 and 9 ('is it valid?' and 'is it
simulatable?') are the ones I'd be looking at/for the most, so if those
bit of the glyphs were emphasized or at least easy to pick out, that'd be
great.

-Lucian

* Catherine Lloyd <c.lloyd at auckland.ac.nz> [2010-06-03 13:27] writes:
> My apologies - my original email was more exclusive to its recipients
> that to the discussion list!
>
> I will be happy to leave this another week to give anyone else a
> change to respond if they have comments.
>
> Best wishes
> Catherine
>
>
>
> >
> >Begin forwarded message:
> >
> >>*From: *Catherine Lloyd <c.lloyd at auckland.ac.nz
> >><mailto:c.lloyd at auckland.ac.nz >>
> >>*Date: *13 May 2010 9:22:00 AM
> >>*To: *biomodels-net-discuss at lists.sourceforce.net
> >><mailto:biomodels-net-discuss at lists.sourceforce.net >
> >>*Cc: *Poul Nielsen <p.nielsen at auckland.ac.nz
> >><mailto:p.nielsen at auckland.ac.nz >>, Tommy Yu <tommy.yu at
> >>auckland.ac.nz
> >><mailto:tommy.yu at auckland.ac.nz>>, David Nickerson
> >><d.nickerson at auckland.ac.nz <mailto:d.nickerson at auckland.ac.nz>>,
> >>Peter
> >> Hunter <p.hunter at auckland.ac.nz <mailto:p.hunter at auckland.ac.nz>>,
> >> Randall Britten <r.britten at auckland.ac.nz
> >> <mailto:r.britten at auckland.ac.nz>>
> >>*Subject: **Curation flags*
> >>
> >>Dear All
> >>
> >>During my last visit to the EBI in August last year I circulated a
> >>document describing the issues we have with the current star system
> >>of curation ratings, and the proposal to replace these stars with
> >>more meaningful curation "flags". Once I was back in Auckland James
> >>Lawson and I went through several iterations of testing out
> >>different flag options, and the topic was also extensively
> >>discussed at the weekly team meetings and also on the Physiome
> >>Tracker (https://tracker.physiomeproject.org/show_bug.cgi?id=87).
> >>Further, the topic was raised at the CellML workshop in February
> >>this year.
> >>
> >>In the end, as the bare minimum (we are happy to add further flags
> >>if needs be), we decided to go with the MIRIAM guidelines (see
> >>attached spreadsheet). This highlighted 2 issues with all the
> >>CellML models in the current repository - 1) None were associated
> >>with a specific terms of use/distribution and 2) None were
> >>annotated with biological data.
> >>
> >>The former has been addressed and we have chosen a creative commons
> >>attribution licence to cover all the data in the repository. Tommy
> >>has been implementing a "terms of use" page and also a "how to cite
> >>this model" page. We'd also like to include the licence term in
> >>the metadata of each model (we have found the correct RDF tag for
> >>this).
> >>
> >>The latter issue is still being addressed. I have annotated 2
> >>CellML models (Goldbeter 1991 and Teusink 2000) but we have to
> >>decide if this is the way we want to annotate models, and if so,
> >>confirm it in the metadata specification. Also until we have
> >>better annotation tools, adding these terms using a text editor is
> >>the only method available and it is less than ideal - that said, I
> >>will be meeting Allyson and Morgan next week to see if it is
> >>possible for me to use Saint to annotate the models. This would be
> >>fantastic from my point of view - BUT - there is then the danger of
> >>me annotating several models in a certain way - only to have to re-
> >>do them later when it's decided the method of annotation has to
> >>change.
> >>
> >>I'll also attend the annotation meeting at the EBI next week.
> >>
> >>I'm circulating this now at the request of the BioModels team, who
> >>are interested in our thoughts on the flags. Ideally the two
> >>efforts would adopt the same set of flags.
> >>
> >>Camille and Lukas looked at our spreadsheets a while ago, and the
> >>attached spreadsheet has been modified in response to their
> >>comments. Additional feedback is always welcome.
> >>
> >>Once we have confirmed the set of flags, Tommy will be able to
> >>start to implement them in the next version of PMR2.
> >>
> >>Best wishes
> >>Catherine
> >>
> >>
> >>
> >
> >>
> >>
> >>
> >>
> >
>

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